The Dubai-based carrier was due to begin operating daily flights to the South African city from 1 December but has decided to re-evaluate how best to use its fleet over the coming months while fuel prices remain at record highs.
The move is a blow to previous claims by the airline that it could survive the current fuel crisis with no impact on its expansion plans.
Many other airlines are planning to ground aircraft to avoid running at a loss on less popular routes.
Emirates already flies 21 times a week to Johannesburg and daily to Cape Town.
Speaking to MEED recently, the executive vice chairman of Emirates, Maurice Flanagan, admitted that although the group made a record profit of AED5.3bn ($1.44bn) in the last financial year, its fuel expenses were $500m more than anticipated (MEED 30:5:08).